The Nautilus is a hard mode boss, only unlocked after beating the game once. It appears after defeating Archeopteryx, and to all intents and purposes it is a pink version of the Dreadnought.
Ironically Nautilus's difficulty doesn't all come from Nautilus itself. Because you need anti submarine weapons, most likely you will have to go back to using a cruiser to be able to hit it (though if you were lucky enough to find an Anti submarine VLS you will be able to use a battleship for the fight). This of course makes the preceding fight against Archeopteryx harder and causing it to most likely drain a lot more of your ammunition than would be helpful. Otherwise it is not too difficult. The storm has passed by this point so visibility is back to normal, and while Nautilus has more powerful weapons than the Dreadnought it is still fairly slow and the overall strategy should be the same.